NM_018076.5:c.2675C>A

Variant names:

• chr10-27862558-G-T
• rs587777049
• NM_018076.5:c.2675C>A

Variant summary

Our verdict is Pathogenic. The variant received 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_018076.5(ODAD2):​c.2675C>A​(p.Ser892*) variant causes a stop gained change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ODAD2 NM_018076.5 stop_gained
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:3
• Conservation: PhyloP100: 7.95
• Publications: 3 publications found

Genes affected

ODAD2 (HGNC:25583): (outer dynein arm docking complex subunit 2) The protein encoded by this gene contains ten Armadillo repeat motifs (ARMs) and one HEAT repeat, and is thought to be involved in ciliary and flagellar movement. This protein has been shown to localize to the ciliary axonemes and at the ciliary base of respiratory cells. Studies indicate that mutations in this gene cause partial outer dynein arm (ODA) defects in respiratory cilia. The cilia of cells with mutations in this gene displayed either reduced ciliary beat frequency and amplitude, or, complete immotility. Some individuals with primary ciliary dyskensia (PCD) have been shown to have mutations in this gene. PCD is characterized by chronic airway disease and left/right body asymmetry defects. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Aug 2015]

ODAD2 Gene-Disease associations (from GenCC):

• primary ciliary dyskinesia 23

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, ClinGen, Labcorp Genetics (formerly Invitae)
• primary ciliary dyskinesia

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Pathogenic. The variant received 18 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 10-27862558-G-T is Pathogenic according to our data. Variant chr10-27862558-G-T is described in ClinVar as Pathogenic. ClinVar VariationId is 66047.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018076.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ODAD2	NM_018076.5	MANE Select	c.2675C>A	p.Ser892*	stop_gained	Exon 18 of 20	NP_060546.2
	ODAD2	NM_001290020.2		c.2675C>A	p.Ser892*	stop_gained	Exon 18 of 20	NP_001276949.1
	ODAD2	NM_001312689.2		c.1751C>A	p.Ser584*	stop_gained	Exon 13 of 15	NP_001299618.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ODAD2	ENST00000305242.10	TSL:1 MANE Select	c.2675C>A	p.Ser892*	stop_gained	Exon 18 of 20	ENSP00000306410.5
	ODAD2	ENST00000673439.1		c.2675C>A	p.Ser892*	stop_gained	Exon 18 of 20	ENSP00000500782.1
	ODAD2	ENST00000672841.1		c.1751C>A	p.Ser584*	stop_gained	Exon 13 of 15	ENSP00000499983.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Primary ciliary dyskinesia 23 Pathogenic:3

Mar 12, 2024

Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: curation

The homozygous p.Ser892Ter variant in ARMC4 was identified by our study in two siblings with congenital fibrosis of the extraocular muscles, global developmental delay, situs inversus, and ciliary dyskinesia, via a collaborative study between the Broad Institute's Center for Mendelian Genomics and the Engle lab (https://kirbyneuro.org/EngleLab/). The p.Ser892Ter variant in ARMC4 has been previously reported in 2 unrelated individuals with primary ciliary dyskinesia 23 (PMID: 24203976, PMID: 23849778) and segregated with disease in 2 affected relatives from one family (PMID: 24203976). These two affected unrelated individuals were homozygotes, which increases the likelihood that the p.Ser892Ter variant is pathogenic. This variant has also been reported in ClinVar (Variation ID: 66047) and has been interpreted as pathogenic by the Lupski Lab of the Baylor College of Medicine and by OMIM. This variant was absent from large population studies. This nonsense variant leads to a premature termination codon at position 892, which is predicted to lead to a truncated or absent protein. Loss of function of the ARMC4 gene is an established disease mechanism in autosomal recessive primary ciliary dyskinesia 23. In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive primary ciliary dyskinesia 23. ACMG/AMP Criteria applied: PVS1, PM2_Supporting, PM3 (Richards 2015).

Jan 01, 2014

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

Apr 03, 2013

Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

This homozygous mutation was predicted to be loss-of-function.

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Pathogenic	0.66
CADD	Pathogenic	42
DANN	Uncertain	1.0
Eigen	Pathogenic	1.0
Eigen_PC	Pathogenic	0.92
FATHMM_MKL	Pathogenic	0.99	D
PhyloP100		8.0
Vest4		0.37
GERP RS		5.9
Mutation Taster		=2/198	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs587777049; hg19: chr10-28151487;